What putty works best on polyester fiberglass sub hulls? I need to fill some sanding marks and also thicker work around new parts to blend them in. I read to stay away from bondo and other polyester base fillers because they do not hold up well to the water. So… what works and yet is sandable?

I find that Polyester fillers work well enough, just make sure you paint them well.

If there are areas of high stress and thermal expansion, you might want to consider reinforcing those sections with some glass tissue or very thin cloth and more polyester resin. Polyester fillers aren't very elastic and have virtually zero tensile or shear strength, and thus tend to crack if subject to those forces.

Epoxy based fillers are much tougher but can be a bit too stiff to work with and take a lot longer to cure.